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Iron in PDB 3qu8: Crystal Structure of A Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with the Inhibitor 4-(4-Nitrobenzyl)Pyridine.

Enzymatic activity of Crystal Structure of A Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with the Inhibitor 4-(4-Nitrobenzyl)Pyridine.

All present enzymatic activity of Crystal Structure of A Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with the Inhibitor 4-(4-Nitrobenzyl)Pyridine.:
1.14.14.1;

Protein crystallography data

The structure of Crystal Structure of A Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with the Inhibitor 4-(4-Nitrobenzyl)Pyridine., PDB code: 3qu8 was solved by M.B.Shah, J.Pascual, C.D.Stout, J.R.Halpert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.51 / 2.80
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 101.880, 101.880, 299.509, 90.00, 90.00, 120.00
R / Rfree (%) 21.8 / 25.9

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of A Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with the Inhibitor 4-(4-Nitrobenzyl)Pyridine. (pdb code 3qu8). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Crystal Structure of A Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with the Inhibitor 4-(4-Nitrobenzyl)Pyridine., PDB code: 3qu8:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 3qu8

Go back to Iron Binding Sites List in 3qu8
Iron binding site 1 out of 6 in the Crystal Structure of A Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with the Inhibitor 4-(4-Nitrobenzyl)Pyridine.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of A Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with the Inhibitor 4-(4-Nitrobenzyl)Pyridine. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:36.0
occ:1.00
FE A:HEM500 0.0 36.0 1.0
NA A:HEM500 2.1 30.8 1.0
NC A:HEM500 2.1 32.6 1.0
NB A:HEM500 2.1 33.2 1.0
ND A:HEM500 2.1 31.3 1.0
SG A:CYS436 2.3 38.5 1.0
NAL A:3QU501 2.3 51.6 1.0
C4C A:HEM500 3.1 31.9 1.0
C1A A:HEM500 3.1 30.0 1.0
C1C A:HEM500 3.1 31.1 1.0
C4A A:HEM500 3.1 31.4 1.0
C1D A:HEM500 3.1 31.2 1.0
C4D A:HEM500 3.1 30.2 1.0
C4B A:HEM500 3.1 34.2 1.0
C1B A:HEM500 3.1 34.3 1.0
CAC A:3QU501 3.2 49.7 1.0
CAD A:3QU501 3.2 52.4 1.0
CHD A:HEM500 3.4 32.2 1.0
CHA A:HEM500 3.4 30.7 1.0
CHC A:HEM500 3.5 33.9 1.0
CHB A:HEM500 3.5 31.9 1.0
CB A:CYS436 3.5 38.2 1.0
CA A:CYS436 4.1 38.4 1.0
C3C A:HEM500 4.2 29.3 1.0
C2C A:HEM500 4.3 29.3 1.0
C2A A:HEM500 4.3 29.4 1.0
C3A A:HEM500 4.3 29.7 1.0
C3B A:HEM500 4.3 35.0 1.0
C2B A:HEM500 4.3 35.6 1.0
C2D A:HEM500 4.3 28.7 1.0
C3D A:HEM500 4.3 30.2 1.0
CAE A:3QU501 4.5 47.6 1.0
CAF A:3QU501 4.6 50.7 1.0
C A:CYS436 4.8 39.0 1.0
N A:LEU437 4.9 39.1 1.0
N A:GLY438 5.0 40.3 1.0

Iron binding site 2 out of 6 in 3qu8

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Iron binding site 2 out of 6 in the Crystal Structure of A Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with the Inhibitor 4-(4-Nitrobenzyl)Pyridine.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of A Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with the Inhibitor 4-(4-Nitrobenzyl)Pyridine. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe500

b:25.5
occ:1.00
FE B:HEM500 0.0 25.5 1.0
NC B:HEM500 1.9 19.7 1.0
NA B:HEM500 2.0 17.4 1.0
NB B:HEM500 2.0 20.1 1.0
ND B:HEM500 2.1 18.8 1.0
SG B:CYS436 2.2 38.2 1.0
NAL B:3QU501 2.3 51.6 1.0
C4C B:HEM500 2.9 20.9 1.0
C4A B:HEM500 2.9 19.9 1.0
C1A B:HEM500 3.0 19.2 1.0
C1C B:HEM500 3.0 20.9 1.0
C1B B:HEM500 3.0 21.6 1.0
C1D B:HEM500 3.1 20.3 1.0
C4D B:HEM500 3.1 19.8 1.0
CAC B:3QU501 3.1 49.7 1.0
C4B B:HEM500 3.1 19.9 1.0
CAD B:3QU501 3.2 52.4 1.0
CHD B:HEM500 3.3 22.5 1.0
CB B:CYS436 3.4 37.9 1.0
CHB B:HEM500 3.4 19.7 1.0
CHA B:HEM500 3.4 18.9 1.0
CHC B:HEM500 3.5 17.8 1.0
C3C B:HEM500 4.1 21.2 1.0
C3A B:HEM500 4.2 21.6 1.0
CA B:CYS436 4.2 38.4 1.0
C2C B:HEM500 4.2 20.3 1.0
C2A B:HEM500 4.2 21.0 1.0
C2B B:HEM500 4.3 20.9 1.0
C3B B:HEM500 4.3 19.7 1.0
C2D B:HEM500 4.3 18.7 1.0
C3D B:HEM500 4.3 21.0 1.0
CAE B:3QU501 4.4 47.6 1.0
CAF B:3QU501 4.5 50.7 1.0
C B:CYS436 4.9 38.9 1.0
CAM B:3QU501 5.0 50.3 1.0
OG1 B:THR302 5.0 54.4 1.0

Iron binding site 3 out of 6 in 3qu8

Go back to Iron Binding Sites List in 3qu8
Iron binding site 3 out of 6 in the Crystal Structure of A Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with the Inhibitor 4-(4-Nitrobenzyl)Pyridine.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of A Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with the Inhibitor 4-(4-Nitrobenzyl)Pyridine. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe500

b:32.7
occ:1.00
FE C:HEM500 0.0 32.7 1.0
NC C:HEM500 1.7 29.8 1.0
NB C:HEM500 1.8 24.9 1.0
ND C:HEM500 1.9 24.4 1.0
NA C:HEM500 1.9 27.1 1.0
SG C:CYS436 2.3 20.0 1.0
NAL C:3QU501 2.4 51.6 1.0
C4C C:HEM500 2.7 27.9 1.0
C1D C:HEM500 2.8 26.9 1.0
C1C C:HEM500 2.8 30.5 1.0
C4B C:HEM500 2.8 25.7 1.0
C1B C:HEM500 2.8 26.9 1.0
C4A C:HEM500 2.9 28.6 1.0
C1A C:HEM500 3.0 27.6 1.0
C4D C:HEM500 3.1 24.0 1.0
CHD C:HEM500 3.1 28.0 1.0
CB C:CYS436 3.2 20.0 1.0
CAC C:3QU501 3.2 49.7 1.0
CAD C:3QU501 3.2 52.4 1.0
CHC C:HEM500 3.3 29.2 1.0
CHB C:HEM500 3.3 26.0 1.0
CHA C:HEM500 3.5 27.1 1.0
C3C C:HEM500 3.9 28.6 1.0
C2C C:HEM500 4.0 27.3 1.0
C3B C:HEM500 4.0 24.4 1.0
C2B C:HEM500 4.0 26.3 1.0
C2D C:HEM500 4.1 25.6 1.0
CA C:CYS436 4.1 30.0 1.0
C3A C:HEM500 4.2 28.9 1.0
C2A C:HEM500 4.2 28.6 1.0
C3D C:HEM500 4.2 23.3 1.0
CAE C:3QU501 4.6 47.6 1.0
CAF C:3QU501 4.6 50.7 1.0
C C:CYS436 4.8 30.0 1.0
N C:GLY438 5.0 39.8 1.0

Iron binding site 4 out of 6 in 3qu8

Go back to Iron Binding Sites List in 3qu8
Iron binding site 4 out of 6 in the Crystal Structure of A Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with the Inhibitor 4-(4-Nitrobenzyl)Pyridine.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of A Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with the Inhibitor 4-(4-Nitrobenzyl)Pyridine. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe500

b:36.2
occ:1.00
FE D:HEM500 0.0 36.2 1.0
NA D:HEM500 2.1 33.2 1.0
NC D:HEM500 2.1 35.6 1.0
NB D:HEM500 2.1 32.9 1.0
ND D:HEM500 2.1 29.9 1.0
SG D:CYS436 2.3 38.5 1.0
NAL D:3QU501 2.3 49.7 1.0
C1A D:HEM500 3.1 33.1 1.0
C4C D:HEM500 3.1 35.3 1.0
C1C D:HEM500 3.1 38.9 1.0
C4A D:HEM500 3.1 34.0 1.0
C4D D:HEM500 3.1 29.7 1.0
C1D D:HEM500 3.1 32.3 1.0
C4B D:HEM500 3.1 36.9 1.0
C1B D:HEM500 3.1 33.1 1.0
CAC D:3QU501 3.2 49.7 1.0
CAD D:3QU501 3.2 47.9 1.0
CB D:CYS436 3.2 38.1 1.0
CHA D:HEM500 3.4 33.5 1.0
CHD D:HEM500 3.4 31.6 1.0
CHC D:HEM500 3.5 39.3 1.0
CHB D:HEM500 3.5 32.9 1.0
CA D:CYS436 4.1 38.3 1.0
C3C D:HEM500 4.3 37.9 1.0
C2C D:HEM500 4.3 38.9 1.0
C2A D:HEM500 4.3 32.1 1.0
C3A D:HEM500 4.3 34.0 1.0
C3B D:HEM500 4.3 35.0 1.0
C2B D:HEM500 4.3 32.2 1.0
C3D D:HEM500 4.3 27.9 1.0
C2D D:HEM500 4.3 32.1 1.0
CAE D:3QU501 4.5 49.7 1.0
CAF D:3QU501 4.5 49.0 1.0
C D:CYS436 4.8 39.1 1.0
N D:GLY438 4.9 40.1 1.0

Iron binding site 5 out of 6 in 3qu8

Go back to Iron Binding Sites List in 3qu8
Iron binding site 5 out of 6 in the Crystal Structure of A Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with the Inhibitor 4-(4-Nitrobenzyl)Pyridine.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of A Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with the Inhibitor 4-(4-Nitrobenzyl)Pyridine. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe500

b:35.1
occ:1.00
FE E:HEM500 0.0 35.1 1.0
NA E:HEM500 2.1 25.5 1.0
NC E:HEM500 2.1 30.2 1.0
NB E:HEM500 2.1 29.1 1.0
ND E:HEM500 2.1 27.2 1.0
NAL E:3QU501 2.3 57.2 1.0
SG E:CYS436 2.3 38.9 1.0
CAC E:3QU501 3.0 55.5 1.0
C4C E:HEM500 3.1 30.9 1.0
C1A E:HEM500 3.1 28.2 1.0
C1C E:HEM500 3.1 32.3 1.0
C4A E:HEM500 3.1 28.1 1.0
C4D E:HEM500 3.1 26.2 1.0
C1D E:HEM500 3.1 25.7 1.0
C4B E:HEM500 3.1 30.8 1.0
C1B E:HEM500 3.1 32.0 1.0
CAD E:3QU501 3.3 57.5 1.0
CB E:CYS436 3.4 38.0 1.0
CHA E:HEM500 3.4 24.3 1.0
CHD E:HEM500 3.4 26.7 1.0
CHC E:HEM500 3.5 30.5 1.0
CHB E:HEM500 3.5 32.7 1.0
CA E:CYS436 4.2 38.3 1.0
C3C E:HEM500 4.2 30.8 1.0
C2C E:HEM500 4.3 32.5 1.0
C2A E:HEM500 4.3 27.9 1.0
C3A E:HEM500 4.3 27.4 1.0
C3B E:HEM500 4.3 33.2 1.0
C2B E:HEM500 4.3 32.2 1.0
C3D E:HEM500 4.3 25.9 1.0
C2D E:HEM500 4.3 25.5 1.0
CAE E:3QU501 4.3 55.6 1.0
CAF E:3QU501 4.6 59.0 1.0
C E:CYS436 4.8 38.8 1.0
CAM E:3QU501 5.0 57.7 1.0

Iron binding site 6 out of 6 in 3qu8

Go back to Iron Binding Sites List in 3qu8
Iron binding site 6 out of 6 in the Crystal Structure of A Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with the Inhibitor 4-(4-Nitrobenzyl)Pyridine.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of A Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with the Inhibitor 4-(4-Nitrobenzyl)Pyridine. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe500

b:61.1
occ:1.00
FE F:HEM500 0.0 61.1 1.0
NC F:HEM500 2.1 63.5 1.0
NA F:HEM500 2.1 63.5 1.0
NB F:HEM500 2.1 64.4 1.0
ND F:HEM500 2.1 64.0 1.0
SG F:CYS436 2.2 41.2 1.0
C4C F:HEM500 3.1 64.7 1.0
C1A F:HEM500 3.1 63.4 1.0
C4A F:HEM500 3.1 65.4 1.0
C1C F:HEM500 3.1 64.8 1.0
C1D F:HEM500 3.1 64.8 1.0
C4D F:HEM500 3.1 65.1 1.0
C1B F:HEM500 3.1 66.1 1.0
C4B F:HEM500 3.1 65.9 1.0
CB F:CYS436 3.4 38.2 1.0
CHD F:HEM500 3.4 65.7 1.0
CHA F:HEM500 3.4 63.6 1.0
CHB F:HEM500 3.5 65.8 1.0
CHC F:HEM500 3.5 65.6 1.0
CA F:CYS436 4.1 38.5 1.0
C2A F:HEM500 4.3 64.0 1.0
C3C F:HEM500 4.3 65.2 1.0
C3A F:HEM500 4.3 66.2 1.0
C2C F:HEM500 4.3 65.9 1.0
C3B F:HEM500 4.3 65.9 1.0
C2B F:HEM500 4.3 66.8 1.0
C2D F:HEM500 4.3 65.6 1.0
C3D F:HEM500 4.3 65.7 1.0
C F:CYS436 4.8 39.2 1.0
CB F:ALA298 4.9 48.0 1.0
N F:GLY438 4.9 40.3 1.0
N F:LEU437 4.9 39.1 1.0

Reference:

M.B.Shah, J.Pascual, Q.Zhang, C.D.Stout, J.R.Halpert. Structures of Cytochrome P450 2B6 Bound to 4-Benzylpyridine and 4-(4-Nitrobenzyl)Pyridine: Insight Into Inhibitor Binding and Rearrangement of Active Site Side Chains. Mol.Pharmacol. V. 80 1047 2011.
ISSN: ISSN 0026-895X
PubMed: 21875942
DOI: 10.1124/MOL.111.074427
Page generated: Sun Aug 4 18:54:28 2024

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